The config/ and build/ directories in js/src/ should be copied from the same files in the root directory. We have a build-time check for this. The build-time check is hidden behind the --with-sync-build-files flag. We should remove the flag and make it non-optional. I'll get to this at some point.
Ah, I see why this is here and is necessary. If we have a spidermonkey-only release, we don't have the root config/ directory to compare to, so we don't want to enable this except when we have that. But it's not a problem, because we run this check when we compile Firefox, so it's on every tryserver build, etc.